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Table 4 Running time (in seconds) of nanoGapFiller for filling the gaps of 12 species

From: Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph

Species #Contigs in assembly graph #Sites in site graph #Edges in site graph #Filled gaps Total length of gaps (nt) Running time (s)
S. ynec 250 774 1905 11 181,832 5.24
S. coelicolor 926 3,532 8160 17 478,321 25.95
S. agal 204 546 5554 16 463,622 8.04
P. syringae 1492 2176 51,343 25 732,210 371.05
P. putida 752 2190 15,759 9 2856,292 188.39
N. farcinica 388 924 2192 19 639,552 10.15
E. coli 734 1348 40,858 23 922,021 88.08
E. carotovora 622 1454 2636 19 586,169 9.42
C. hutchinsonii 596 990 5105 25 895,179 12.24
B. pseudomallei 390 2144 2662 8 175,737 3.83
B. japonicum 992 3524 26,014 29 1021,611 1721.27
A. vari 870 474 135,667 17 4917,178 71,067.07
  1. Here, the gaps are identified using simulated optical maps with alignment method SOMA2. CPU: AMD Opteron 6344; OS: Ubuntu 16.04; Python version: 3.6.7